Examining The Two Branches Of Nucleic Acids Biology Essay

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Nucleic acids are an acidic substances present in the nuclei of cells and carry genetic information in the cells. The nucleic acid consists of two branches, nucleotide and nucleoside. When all three components of the nucleic acid, that is sugar, phosphate, and bases are present in a molecule, then it is called nucleotide and nucleoside when phosphate is absent. In cellular metabolism nucleotide have variety of roles. They are energy currency in metabolic exchanges, the essential chemical links in the response of cells to hormones and other stimulating agents, structural components of an array of enzyme cofactors and metabolic intermediates. Most importantly, nucleotides are the constituent of nucleic acid; deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), the molecular repositories of genetic information. The structure of every protein, cellular component, is a ultimate result of information programmed in the nucleotide sequence of a cell's nucleic acids. "The ability to store and transmit genetic information from one generation to the next is a fundamental condition for life."

Deoxyribonucleic Acid (DNA)

Deoxyribonucleic Acid is a macromolecule found in all living cells specifically in the chromosome and few in cytoplasm as well in the mitochondria and chloroplasts. It is usually double stranded structure and single strand in few viruses like Parvovirus. The DNA was first isolated by the Swiss Physician Friedrich Miescher in 1969, and he discovered in a small substance in the pus of discarded surgical bandages. Phoebus Levene identified base, sugar, and phosphate as nucleotide units in the year 1919.

Deoxyribonucleic Acid, (n.d)

Structure of Deoxyribonucleic Acid (DNA)

The most accepted and the exact structure of the Deoxyribonucleic Acid was first introduced by J.D.Watson and F.H.C.Crick in the year 1953.They deduced that DNA is double helix structure .The deduction was based on two major evidences:

They observed that amount of Thymine is always equal to amount of Adenine and cytosine with guanine. This is known as Chagaff's rule. (Garner,2005)

By the X-ray diffraction pattern of Wilkens and Franklin showed that the Deoxyribonucleic Acid molecule are helical structure with repeating units of base at every 0.34nm.

(Nelson et al, 2000)

The double helix structure of the DNA is shown below:

Figure 1: The double helix structure of DNA.

Double helix structure of DNA, (n.d)

DNA is a long polymer made from repeating units called nucleotide. The Deoxyribonucleic Acid chain is 20 Angstroms wide (2.0 nm), and one nucleotide unit is 3.4 Š(0.34 nm) long. The DNA double structure is made of two polypeptide chain is in turn made of several nucleotides which constitute of sugar, phosphate as backbone and base pairs as complementary to each other which form hydrogen bonding. The double helix structure of DNA is right handed structure. (Gardner et al, 2005).The backbone of the DNA strand is made from alternating phosphate and sugar. The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate group's forms a phosphodiester bond between the third and fifth carbon atom of the sugar ring. The two polypeptide chain runs opposite direction. One strand runs form three prime carbon of nucleotide to a five prime carbon of the other nucleotide and other from five prime to three prime carbons, collectively called as anti-parallel. In the double helix structure, the sugar phosphate (backbone) structure follow helical path toward the outer edge and the bases in the central. The spiral coiling of the chain around each other result in the formation of major and minor grooves. (Becker et al, 2006) As mentioned, the polypeptide chain is made of several nucleotides and nucleotides are made of three components as shown below:

Deoxyribonucleic Acid

Sugar(Deoxyribose)

Phosphate

Heterocyclic Bases

Purine

Pyrimidine

Adenine (A)

Guanine (A)

Cytosine(C)

Thymine (T)

(Gardner et al, 2005)

The structure of each components of nucleotide:

1) Deoxyribose Sugar 2) phosphate

3) Bases

a) Purine

Adenine (A) Guanine (G)

b)Pyrimidine

Cytosine(C) Thymine (T)

Figure 2: Components of DNA nucleotide. (Bender, 2005)

Function of DNA

The Double helix nature of the DNA accomplishes a unique function to store and transmit genetic information over long period of time.

The structure of DNA determine the function

The base pairing of A with T and G with C makes the possibility of exact duplication of DNA that store exact information to inherited to the offspring and the absence of OH group in DNA help to prevent from formation of cyclic phosphate ester, and in turn prevented from hydrolization by alkali. The DNA is methylated to one of the Pyrimidine base thymine which is helpful in prevent attacking from the enzymes nuclease. The double nature of DNA provides protection against the chemical attack because of the hydrogen bonding between bases provide the first line of the defense, since bases are hydrophobic, they stack together and make a surface non-susceptible to the chemical attack to the DNA. All the bases are stacked upon one another in the central region of the DNA, in doing so, water is excluded from stack of the bases, where this is "dry" region of the bases makes any water soluble compounds difficult to reach bases and disrupt it. (Gardner, et al, 2005) The DNA is design in such a way that it forms major and minor grooves which plays important role in interaction with variety of molecule with DNA. (Becker, et al, 2006). The presence of sugar "Deoxyribose" in the polypeptide chain makes carbon to carbon bonds which are much resistant to the chemical attack under all conditions except at certain strong acids at high temperature. The N-glycosidic bond between the base -sugar and larger number of hydrogen bonding helps in stability of the DNA. (Gardner et al, 2005)

Ribonucleic Acid (RNA)

Ribonucleic Acid is mainly found in the cytoplasm of the cell. RNA is mostly non genetic and it act as genetic material in some plant viruses like Tobacco Mosaic viruses. The basic structure of RNA is similar with few differences and RNA is mostly single stranded.

Structural differences of RNA with DNA

RNA and DNA are both nucleic acids, but differ in three main ways. Firstly, unlike DNA which is double-stranded, RNA is a single-stranded molecule and has a much shorter chain of nucleotides. Secondly, DNA contains deoxyribose; where as RNA contains ribose (DNA lacks hydroxyl group attached to the pentose ring in the 2' position). This OH group makes RNA less stable than DNA because it is more susceptible to hydrolysis. Thirdly, the complementary base to adenine is not thymine in RNA, but rather uracil, which is an unmethylated form of thymine. (Lodish, 2008). In RNA, nucleotides in the chain are joined by3 , 5 phosphodiester bonds.

Figure 3: Chemical structure of RNA

Ribonucleic Acid (n.d)

The single polypeptide chain of RNA is made of three components as DNA except one of the bases of Pyrimidine is replaced by Uracil. The components of ribonucleotide are shown below:

Ribonucleic Acid

Sugar (Ribose)

Phosphate

Heterocyclic Bases

Purine

Pyrimidine

Adenine (A)

Guanine (A)

Cytosine(C)

Uracil (U)

(Becker et al, 2006) & (Gardner et al, 2005)

The structure that are different from DNA are shown below and other components are as same as DNA as shown in (figure 2) except sugar and one of the pyrimidine base as mentioned above and shown below.

Sugar (Ribose) 2) Bases (Pyrimidine)

Uracil (U)

Figure 4: Ribose sugar and Uracil. (Bender, 2003)

The function of RNA

RNA does the translation of the information stored in DNA in to amino acid sequence of protein. In translation the DNA serve as template and work according to the mRNA and the tRNA carry particular amino acid to participate in the process of translation. The rRNA is the major needs of the ribosome for the protein synthesis and provides specific binding sites for the protein synthesis. (Hartl, 2001) The RNA provides selective binding with other molecules because of its single stranded structure provides flexibility of bending back on to itself allows one parts of the molecules to form a weak hydrogen bonding with the other part of same molecules. (Alberts, 2008)

Type of RNA and functions based on their structure:

A) Messenger RNA

The information stored in the DNA is copied into mRNA, since the mRNA is transcribed on DNA; its base sequence is complementary to that of the segment of DNA on which it is transcribed mRNA has five prime cap and the poly (A) tail that help proper binding of the mRNA to the ribosome (Eukaryotes).when the single mRNA is used for coding a gene called monocistronic (eukaryotes) and coding for more than one is called polycistronic (Prokaryotes).It has starting codon AUG and stop codon AUG,UGA,UUG.(Becker et al, 2006)

Figure 5: structure of mRNA (Eukaryotes)

(Becker et al, 2006) & (Harlt et al, 2005)

Function of mRNA

The mRNA carries information on the sequence of amino acid for the protein synthesis. The 5  cap in mRNA provides protection from the nuclease that attack the RNA at 5 end and also position mRNA on the ribosome for initiation of translocation especially in eukaryotes. The poly (A) tail provides protection against the nuclease attack and interacts with specific protein involved in transporting mRNA to cytoplasm. It also helps to transcribe the mRNA molecule. DNA has useless introns (Eukaryotes), so that mRNA is necessary in the removal of introns by spliceosome. (RNA protein complex) (Becker et al, 2006)& (Bhagavan, 2002)

B) Transfer RNA

Transfer RNA is RNA molecule has inverted 'L' structure or clover leaf structure. It has anti-codon loop that make base pair with the mRNA for specific amino acids. Amino acids are bind to tRNA through ester linkage to the three prime OH by particular mRNA to form charged tRNA.This activated tRNA with the mRNA codes at the peptidyl binding site and the aminoacyl binding site of the ribosomes.( Becker et al, 2006)

Figure 6: Secondary structure of tRNA

Secondary structure of tRNA (n.d)

Function of tRNA

When the information of mRNA reaches to tRNA it brings translation of mRNA sequence into amino acid sequence of the protein. The L-shaped tertiary structure maximizes the length of the base pairs by stacking them into two sets forming long extended region. The two parts of each the extended region are not aligned perfectly and thus it bends slightly. This alignment allows the base pairs to stack on each other and provide stability. (Weaver, 2002) The folded nature of the anti-codon backbone into particular shape provides base pairing with corresponding codons. The twisted structure of the tRNA is said to provide its decoding function when necessary. The attachment of the amino acid to tRNA through ester linkage to the 3΄ OH to form activated or charged tRNA and this charged tRNA is responsible for pairing with mRNA codons in appropriate site of the protein. The charged tRNA recognizes appropriate codon with mRNA in the peptidyl site (P) and aminoacyl site (A) of the ribosome and leave through exit site. (Weaver, 2002)

C) Ribosomal RNA

Ribosomal RNA, the name suggests it is found in the ribosome. In the cells that are synthesizing proteins, electron micrographs has shown that ribosomes are associated in a bead like string called poly-ribosomes formed by the attachment of the ribosomes to a single molecule of mRNA.The ribosomal units in the prokaryotes are 70s ribosomes and 80s in eukaryotes . This ribosome's are further dissociated into subunits of 50s and 30s in prokaryotes and 60s and 40s in eukaryotes, because mRNA of the initiating aminoacyl tRNA cannot bind directly to 70s and 80s ribosomes. (Ahluwalia, 1985)

. Function of rRNA

rRNA is used in building the ribosome's and that moves along the mRNA and the binding of ribosome with the mRNA take place at 5  end of the mRNA as shown in the (fig 5) and it checks the suitable code of mRNA.The mRNA and tRNA carrying the first amino acid bind to smaller ribosomal subunit in its proper orientation by means of special nucleotide sequence called mRNAs ribosome binding site, also known as shine -Dalgarno sequence.

(Lodish et al, 2008)

General function of RNA based on the structure:

RNA structure has an OH-group attached at the 2´carbon of ribose and this 2´-hydroxyl group in RNA acts as nucleus loving, attacking the phosphodiester bond. It results in less chance of storing the information. On the other hand this hydroxyl group on carbon two of ribose makes RNA more liable by attacking and hydrolysis the phosphodiester bond at around PH 7. This stability divides RNA into mononucleotides by alkaline solution. The carbon two hydroxyl group of RNA provides a chemically reactive group that takes part in RNA- mediated catalysis and as a result RNA like ribosomal RNA plays a catalytic role in the formation of peptide bond, by exact sequencing the amino acids during protein synthesis and flow of information is accurate. (Lodish et al, 2008) .Presence of Uracil in RNA gets easily folded forming secondary structure. During folding, Uracil gets pair with adenine in which they will stabilize the secondary structure of RNA. Its presence also helps in enhancing the smooth flow of genetic information in the exact sequence of amino acids during protein synthesis. Uracil is also a reactive base since it does not have a methyl group that prevents the renaturation of helix and organism receives immediate genetic information. (Lodish et al, 2008). Beside this single stranded structure also provide flexibility in bending and form weak hydrogen bond with same part of molecules and provide selective binding with other molecules. (Alberts et al, 2008)

Thus, DNA and RNA are the important molecular repositories for genetic information because they store and transmit information form one generation to other over long period of time and can bring in evolution.

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